I love your ambition, OpenGL is a very low starting point these days.
The jMonkeyEngine you are talking about is probably a good way to get started. This will help you with bulk code loading.
One important thing in the case of a game / 3d programming is that even if you have a high-level mechanism, you may want to make some animations, some shaders, etc., requiring detailed knowledge in the rendering pipeline, detailed knowledge about the vector math and those things. You cannot get around this, but I suggest you “take” open source.
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